Re: [AMBER] Question on Updating AMBER

From: Jason Swails <>
Date: Tue, 19 Aug 2014 08:51:45 -0400

On Tue, 2014-08-19 at 08:18 -0400, Gulsevin,Alican wrote:
> Hello,
> I was running some calculations involving a) PMEMD, b) Quasi-Harmonic
> Analysis and AMBER14 stopped working, giving GpuBuffer errors first for
> the PMEMD calculations, only killing the Quasi-Harmonic analysis jobs
> without giving any warnings. After this, I thought updating AMBER might
> be a good idea, for some of the newer patches contain fixes for cpptraj
> and I am using, which could help.
> When I try to update amber by ./update_amber --update command, I get
> the following answer:
> Preparing to apply updates... please wait.
> Applying AmberTools 14/update.1
> instance: .patches/AmberTools14_Unapplied_Patches/update.1 failed to
> apply. No changes made from this patch

What this means is that the files that update.1 modifies have already
been modified in a way that is incompatible with that patch. There are
a number of ways this can happen, so if you know how it happened and can
reverse those changes, you will need to do that before updating.

If not, you can start over with a fresh copy of Amber 14 and AmberTools


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Aug 19 2014 - 06:00:03 PDT
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